itkPhilipsPAR.h

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/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkPhilipsPAR.h,v $
  Language:  C++
  Date:      $Date: 2009-04-29 12:17:28 $
  Version:   $Revision: 1.5 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/

#ifndef __itkPhilipsPAR_h
#define __itkPhilipsPAR_h

#include <stdio.h>
#include <stdlib.h>
#include <string>
#include "itkLightProcessObject.h"
#include "itkVectorContainer.h"
#include "vnl/vnl_vector_fixed.h"

#define RESEARCH_IMAGE_EXPORT_TOOL_V3       30
#define RESEARCH_IMAGE_EXPORT_TOOL_V4       40
#define RESEARCH_IMAGE_EXPORT_TOOL_V4_1     41
#define RESEARCH_IMAGE_EXPORT_TOOL_V4_2     42
#define RESEARCH_IMAGE_EXPORT_TOOL_UNKNOWN  -1

#define PAR_DEFAULT_STRING_LENGTH           32
#define PAR_DEFAULT_TRIGGER_TIMES_SIZE      128
#define PAR_DEFAULT_ECHO_TIMES_SIZE         128
#define PAR_DEFAULT_REP_TIMES_SIZE          128
#define PAR_DEFAULT_IMAGE_TYPES_SIZE        8
#define PAR_DEFAULT_SCAN_SEQUENCE_SIZE      8
#define PAR_RESCALE_VALUES_SIZE             3
#define PAR_DIFFUSION_VALUES_SIZE           3

#define PAR_SLICE_ORIENTATION_TRANSVERSAL   1
#define PAR_SLICE_ORIENTATION_SAGITTAL      2
#define PAR_SLICE_ORIENTATION_CORONAL       3

namespace itk
{

struct par_parameter  //par_parameter
{
  int problemreading; // Marked 1 if problem occurred reading in PAR file
  int ResToolsVersion; // V3, V4, V4.1, or V4.2 PAR/REC version
  char patient_name[PAR_DEFAULT_STRING_LENGTH]; // Patient name
  char exam_name[PAR_DEFAULT_STRING_LENGTH]; // Examination name
  char protocol_name[PAR_DEFAULT_STRING_LENGTH]; // Protocol name
  char exam_date[PAR_DEFAULT_STRING_LENGTH]; // Examination date/time
  char exam_time[PAR_DEFAULT_STRING_LENGTH]; // Examination date/time
  char series_type[PAR_DEFAULT_STRING_LENGTH]; // Series Type
  int scno; // Acquisition nr
  int recno; // Reconstruction nr
  int scan_duration; // Scan Duration [sec]
  int cardiac_phases; // Max. number of cardiac phases
  float trigger_times[PAR_DEFAULT_TRIGGER_TIMES_SIZE]; // trigger_time (float)
  int echoes; // Max. number of echoes
  float echo_times[PAR_DEFAULT_ECHO_TIMES_SIZE]; // Echo times read from PAR file
  int slice; // Max. number of slices/locations
  int dyn; // Max. number of dynamics
  int mixes; // Max. number of mixes
  char patient_position[PAR_DEFAULT_STRING_LENGTH]; // Patient position
  char prep_direction[PAR_DEFAULT_STRING_LENGTH]; // Preparation direction
  short int bit; // Image pixel size [8 or 16 bits]
  char technique[PAR_DEFAULT_STRING_LENGTH]; // Technique
  char scan_mode[PAR_DEFAULT_STRING_LENGTH]; // Scan mode
  int num_averages; // Number of averages
  int scan_resolution[2]; // Scan resolution  (x, y)
  int scan_percent; // Scan percentage
  int dim[3]; // Recon resolution (x, y) + slices (z)
  float repetition_time[PAR_DEFAULT_REP_TIMES_SIZE]; // Repetition time [msec]
  int sliceorient; // slice orientation ( TRA/SAG/COR ) (integer)
  float slth; // Slice thickness [mm]
  float gap; // Slice gap [mm]
  float fov[3]; // FOV (ap,fh,rl) [mm]
  float water_fat_shift; // Water Fat shift [pixels]
  float angAP; // Angulation midslice(ap,fh,rl)[degr]
  float angFH; // Angulation midslice(ap,fh,rl)[degr]
  float angRL; // Angulation midslice(ap,fh,rl)[degr]
  float offAP; // Off Centre midslice(ap,fh,rl) [mm]
  float offFH; // Off Centre midslice(ap,fh,rl) [mm]
  float offRL; // Off Centre midslice(ap,fh,rl) [mm]
  int flow_comp; // Flow compensation <0=no 1=yes> ?
  int presaturation; // Presaturation     <0=no 1=yes> ?
  int cardiac_freq; // Cardiac frequency
  int min_rr_int; // Min. RR interval
  int max_rr_int; // Max. RR interval
  float phase_encode_vel[3]; // Phase encoding velocity [cm/sec]
  int mtc; // MTC               <0=no 1=yes> ?
  int spir; // SPIR              <0=no 1=yes> ?
  int epi; // EPI factor        <0,1=no EPI>
  int turbo; // TURBO factor      <0=no turbo>
  int dynamic_scan; // Dynamic scan      <0=no 1=yes> ?
  int diffusion; // Diffusion         <0=no 1=yes> ?
  float diff_echo; // Diffusion echo time [msec]
  float inversion_delay; // Inversion delay [msec]
  int max_num_diff_vals; // Max. number of diffusion values
  int max_num_grad_orient; // Max. number of gradient orients
  int num_label_types; // Number of label types   <0=no ASL>
  float vox[3]; // pixel spacing (x,y) (in mm)
  int slicessorted; // 1-slices sorted, 0-slices not sorted
  int image_blocks; // The total number of image blocks stored in the REC file
  int num_image_types; // The number of image types in the REC file
  int image_types[PAR_DEFAULT_IMAGE_TYPES_SIZE]; // The different image types 
                                                 // detected in the REC
  int num_scanning_sequences; // The number of scanning sequences in the REC file
  int scanning_sequences[PAR_DEFAULT_SCAN_SEQUENCE_SIZE]; // The different 
                                                          // scanning sequences 
                                                          // detected in the REC
  int num_slice_repetitions; // If num_scanning_sequences > 1 then 
                  // num_image_types may not equal the total number of slice 
                  // repetitions for a single acquisition.  This value is the 
                  // total number of slice repetitions for a single acquisition 
                  // and is valid only when slicessorted == 0.

};

class ITK_EXPORT PhilipsPAR : public LightProcessObject
{
public:
  typedef PhilipsPAR         Self;
  typedef LightProcessObject Superclass;
  typedef SmartPointer<Self> Pointer;

  itkNewMacro(Self);

  itkTypeMacro(PhilipsPAR, Superclass);

  // Reads the PAR file parameters in "parFile" and stores the PAR parameters in 
  // pPar.
  // Returns false if an error is encountered during reading, otherwise true is 
  // returned.
  void ReadPAR(std::string parFile, struct par_parameter* pPar);

  // Returns a vector of paired values, the first contains the slice index and the 
  // second is the image type for the PAR file "parFile".
  typedef std::pair< int, int >                 PARSliceIndexImageType;
  typedef std::vector< PARSliceIndexImageType > PARSliceIndexImageTypeVector;
  PARSliceIndexImageTypeVector GetRECSliceIndexImageTypes(
    std::string parFile);

  // Returns a vector of paired values, the first contains the slice index and the 
  // second is the scan sequence for the PAR file "parFile".
  typedef std::pair< int, int >                    PARSliceIndexScanSequence;
  typedef std::vector< PARSliceIndexScanSequence > PARSliceIndexScanSequenceVector;
  PARSliceIndexScanSequenceVector GetRECSliceIndexScanningSequence(
    std::string parFile);

  // Returns a vector of paired values, the first contains the image type and the 
  // second is the scan sequence for that image type for the PAR file "parFile".
  typedef std::pair< int, int >                   PARImageTypeScanSequence;
  typedef std::vector< PARImageTypeScanSequence > PARImageTypeScanSequenceVector;
  PARImageTypeScanSequenceVector GetImageTypesScanningSequence(
    std::string parFile);

  // Stores rescale values in the VectorContainer "rescaleValues" for each image 
  // type of the specified scan sequence number "scan_sequence" (from 
  // scanning_sequences) for the PAR file "parFile".
  // Returns false if an error is encountered during reading, otherwise true is 
  // returned.
  typedef vnl_vector_fixed< double, PAR_RESCALE_VALUES_SIZE > 
  PARRescaleValues;
  typedef VectorContainer< unsigned int, PARRescaleValues > 
  PARRescaleValuesContainer;
  bool GetRECRescaleValues(std::string parFile,
    PARRescaleValuesContainer *rescaleValues, int scan_sequence);

  // Stores the diffusion gradient values in the VectorContainer "gradientValues" 
  // and the diffusion b values in the VectorContainer "bValues" for each gradient 
  // direction in the PAR file "parFile".  This function is applicable only for PAR
  // versions > 4.1
  // Returns false if an error is encountered during reading, otherwise true is 
  // returned.
  typedef vnl_vector_fixed< double, PAR_DIFFUSION_VALUES_SIZE > 
  PARDiffusionValues;
  typedef VectorContainer< unsigned int, PARDiffusionValues >
  PARDiffusionValuesContainer;
  typedef VectorContainer< unsigned int, double > 
  PARBValuesContainer;
  bool GetDiffusionGradientOrientationAndBValues(std::string parFile,
    PARDiffusionValuesContainer *gradientValues, PARBValuesContainer *bValues);

  // Returns a vector of ASL label types for the PAR file "parFile".
  typedef VectorContainer< unsigned int, int > PARLabelTypesASLContainer;
  bool GetLabelTypesASL(std::string parFile,
    PARLabelTypesASLContainer *labelTypes);

  // Read a line number within the PAR file.
  std::string GetLineNumber(std::string file, int lineNum);

protected:
  PhilipsPAR();
  ~PhilipsPAR();
  void PrintSelf(std::ostream& os, Indent indent) const;

private:
  PhilipsPAR(const Self&); //purposely not implemented
  void operator=(const Self&); //purposely not implemented

  int GetPARVersion(std::string parFile);

  std::string GetGeneralInfoString(std::string file, int lineNum);

  std::string m_FileName;

  std::vector<std::string> m_PARFileLines;

};

} // end namespace itk

#endif                           /* __itkPhilipsPAR_h */

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